Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

93 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Chromatin accessibility of a model of CRISPR-mediated insulator disruption in the MMP locus in triple-negative breast cancer cell lines

ABSTRACT: Using CRISPR-Cas9 technology, we stably disrupted an insulator element in two different TNBC cell lines. The aim of this experiment was to characterize the chromatin accessibility profile using ATAC-seq. For this experiment, we selected three biological replicates of MDA-MB-231 (WT and IE8dis) and MDA-MB-436 (WT and IE8dis).

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: Miquel Ensenyat-Mendez

PROVIDER: E-MTAB-12821 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Chromatin architecture profiling of a model of CRISPR-mediated insulator disruption in the MMP locus in triple-negative breast cancer cell lines

Project description:Using CRISPR-Cas9 technology, we stably disrupted an insulator element in two different TNBC cell lines. The aim of this experiment was to characterize the chromatin architecture profile using Hi-C. For this experiment, we selected three biological replicates of MDA-MB-231 (WT and IE8dis).

2023-08-31 | E-MTAB-12825 | biostudies-arrayexpress

ATAC-seq on endocardial cells from E12.5 mouse hearts in Tbx20 knockouts and wild type counterparts

Project description:We used ATAC-seq (Buenrostro et al, 2013) to identify regions of open chromatin in FACS sorted mouse endothelial cells from E12.5 hearts. Please note that the animals were injected at different dates, which resulted in different effects of the knockout, as indicated in the batch attribute of the samples. This data set is part of the study \Endocardial Tbx20 is essential for mesenchymal and myocardial cell movements required for cardiac septation\. Peaks were called using HOMER (-gsize 1.87e9 -region -tbp 1). Replicate 1: -fdr 1e-8, replicate 2: default parameters. Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ. 2013. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods 10: 12138.

2017-06-02 | E-MTAB-3972 | biostudies-arrayexpress

Gene expression profiling of a model of CRISPR-mediated insulator disruption in the MMP locus in triple-negative breast cancer cell lines

Project description:Using CRISPR-Cas9 technology, we stably disrupted an insulator element in two different TNBC cell lines. The aim of this experiment was to characterize the transcriptomic profile using RNA-seq. For this experiment, we selected three biological replicates of MDA-MB-231 (WT and IE8dis).

2023-08-31 | E-MTAB-12823 | biostudies-arrayexpress

ATAC-seq of CP-A Barrett's oesophagus cells

Project description:The open chromatin of Barrett's oesophagus cell line CP-A has been profiled by ATAC-seq.

2020-09-30 | E-MTAB-8994 | biostudies-arrayexpress

ATAC-seq of Oesophageal Cell Lines

Project description:ATAC-seq in oesophageal cell lines, OE33 (OAC), FLO1 (OAC), HET1A (Normal)

2016-09-12 | E-MTAB-4209 | biostudies-arrayexpress

ATAC-seq of human Barrett's oesophagus tissue

Project description:Barrett's esophagus is the assumed precusor to oesophageal adenocarcinoma. We profiled the open chromatin of human Barrett's biopsies to gain insight into its molecular basis.

2019-02-04 | E-MTAB-6751 | biostudies-arrayexpress

ATAC-seq in control compared to ZEB1 knock-down MDA-MB-231 cells

Project description:Identification of open chromatin regions in wildtpye, control knock-down (shCtrl) and ZEB1 knock-down (shZEB1) human breast cancer MDA-MB-231 cells by ATAC(Assay for transposable-accessible chromatin)-seq.

2020-07-22 | E-MTAB-8264 | biostudies-arrayexpress

ATAC-seq of oesophageal adenocarcinoma cell line MFD-1

Project description:The open chromatin of new esophageal adenocarcinoma cell line MFD-1 has been profiled by ATAC-seq.

2018-04-06 | E-MTAB-6720 | biostudies-arrayexpress

ATAC-seq of Het1A cells with overexpression of HNF4A or GATA6

Project description:To determine the ability of HNF4A and GATA6 to drive open chromatin formation, either HNF4A or GATA6 were overexpressed in normal oesophageal Het1A cells and ATAC-seq was performed.

2019-02-04 | E-MTAB-6931 | biostudies-arrayexpress

Metabolic and lipidomic characterization of radioresistant MDA-MB-231 human breast cancer cells to investigate potential therapeutic targets

Project description:To provide preliminary insights into metabolic and lipidomic characteristics in radioresistant triple-negative breast cancer (TNBC) cells and suggest potential therapeutic targets, we performed a comprehensive metabolic and lipidomic profiling of radioresistant MDA-MB-231 (MDA-MB-231/RR) TNBC cells and their parental cells using gas chromatography-mass spectrometry and nano electrospray ionization-mass spectrometry, followed by multivariate statistical analysis. Buthionine sulfoximine (BSO) and radiation were co-treated to radioresistant TNBC cells. The level of glutathione (GSH) was significantly increased, and the levels of GSH synthesis-related metabolites, such as cysteine, glycine, and glutamine were also increased in MDA-MB-231/RR cells. In contrast, the level of lactic acid was significantly reduced. In addition, reactive oxygen species (ROS) level was decreased in MDA-MB-231/RR cells. In the lipidomic profiles of MDA-MB-231/RR cells, the levels of phosphatidylcholine (PC) and phosphatidylethanolamine (PE) were significantly increased, whereas those of most of the phosphatidylinositol species were significantly decreased. BSO sensitized MDA-MB-231/RR cells to radiotherapy, which resulted in decreased GSH level and increased ROS level and apoptosis. Radioresistant TNBC cells showed distinct metabolic and lipidomic characteristics compared to their parental cells. We suggested activated GSH, PC, and PE biosynthesis pathways as potential targets for treating radioresistant TNBC cells. Particularly, enhanced radiosensitivity was achieved by inhibition of GSH biosynthesis in MDA-MB-231/RR cells.

2021-09-22 | ST001920 | MetabolomicsWorkbench

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data